Issues after motherboard replacement

Hi,

My Dell XPS 13 9360 started shutting down randomly and I figured out the motherboard needed replacing. After installing the new motherboard, I could not switch on the laptop. Reinstalling the BIOS fixed it and I was able to start Windows. 

Everything works fine except the USB-C on the left side and the USB-B and card reader on the right side (USB-B on the left side works). The light on the power button doesn't work either. Also, anytime I shut off my laptop it won't turn on with the power button. If I ctrl+esc while plugging in the charger then I get a 'Recovery Image not found' warning light. The only way to start it is to insert the external USB with the BIOS install file on it while pressing ctrl+esc. Then I just exit the BIOS recovery screen and it boots into windows. I always just put my laptop into sleep mode instead of shutting it down now. 

I am nearly sure this is some sort of software thing. I have updated everything (BIOS, Windows, Drivers) and the hardware diagnostics didn't find any errors. Any advice?